BOSC 2009 Schedule

Return to BOSC 2009 main page.

Keynote Speakers

The BOSC 2009 Organizing committee is pleased to announce our two Keynote Speakers:

Alan Ruttenberg

Alan Ruttenberg is a Principal Scientist at Science Commons. He works with Semantic Web technologies in computational biology, with an emphasis on the creation and application of structured biological knowledge to interpret experimental results. He is currently involved in a number of open biomedical ontology efforts, including: the Ontology for Biomedical Investigations (OBI), the Basic Formal Ontology (BFO) that will form the upper level ontology for the OBO foundry, the Infectious Disease Ontology (IDO), the Program on Ontologies of Neural Structures (PONS), the Information Artifact Ontology (IAO), and BioPAX-OBO for representing molecular and cellular pathways. These interests and efforts come together in my project at Science Commons - the Neurocommons, a large scale Semantic Web knowledge base of biological information aimed at supporting, initially, the neurosciences. He is also an active participant in W3C Semantic Web activities. In 2006 and 2007 he was a member of the Health Care Life Sciences Interest Group, and early work on the Neurocommons became the core of the prototype life sciences knowledge base that the group has documented. He is a chair of the OWL Working Group specifying OWL 2, and a coordinating editor of the OBO Foundry. His graduate work was at the MIT Media Lab in the Music and Cognition Group, and he has an undergraduate degree in Physics and Mathematics from Brandeis University.

Robert S. Hanmer

Robert S. Hanmer is a Consulting Member of Technical Staff in the Technical Component Management area in Alcatel-Lucent’s Operations area. He is based in Naperville, Illinois, USA. Current responsibilities include developing software-sourcing strategies for middleware and open source software. Previous positions within Lucent and Bell Laboratories have included development, architecture and evaluation of highly reliable systems focusing especially on the areas of reliability and performance. He is active in the software patterns community, including serving as program chair at several pattern conferences. He has authored or co-authored 14 journal articles, several book chapters and the book Patterns for Fault Tolerant Software. He is a member of the IEEE Computer Society, a Senior Member of the ACM and current President of The Hillside Group, the organization that sponsors the PLoP conference. He received his B.S. and M.S. degrees in Computer Science from Northwestern University in Evanston, Illinois.

His talk at BOSC will be entitled "Software Patterns for Reusable Design".

Multicore & GPGPU Computing

Click on the title to view the abstract.

• Jean-Stéphane Varré - Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics (15 min.)
• Josh Buckner - Enabling GPU Computing in the R Statistical Environment (15 min.)
• Mikhail Fursov - UGENE – A practical approach for complex computational analysis in molecular biology (10 min.)
• Oswaldo Trelles - Qnorm: A library of parallel methods for gene-expression Q-normalization (5 min. Lightning Talk)

Computational Grids

Click on the title to view the abstract.

• Hajo N. Krabbenhöft - Taverna workflows across Grids, web services and the command line (15 min.)
• Ann-Kristin Grimm - Grid-based expression QTL analysis (10 min.)
• Joel Hedlund - The Nordic BioGrid project -- Bioinformatics for the grid (5 min. Lightning Talk)

Visualization

Click on the title to view the abstract.

• Allan Kuchinsky - Cytoscape Springs Forward: Re-architecture for Version 3.0 (15 min.)
• Frederik Decouttere - Bioinformatics simplified with seqpad (10 min.)
• Bernat Gel - DASGenExp: an interactive web-based DAS client with client-side rendering (10 min.)

Open Source Software

Click on the title to view the abstract.

• Kazuharu Arakawa - Web Service Interface for G-language Genome Analysis Environment (10 min.)
• Sylvain Brohée - Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases (10 min.)
• Quinn Snell - PSODA: Open Source Phylogenetic Search and DNA Analysis (15 min.)

Data & Analysis Management (shared session with D&AM SIG)

Click on the title to view the abstract.

• Morris Swertz - MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments (15 min.)
• Mark Welsh - BioHDF: Open binary file formats for large-scale data management – Project Update (15 min.)
• Robert Murphy - PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions (15 min.)
• Kam Dahlquist - XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources (10 min.)
• Brad Chapman - Lowering barriers to publishing biological data on the web (10 min.)

Bio* Update

Click on the title to view the abstract.

• Martin Senger - Soaplab: Open Source Web Services Framework for Bioinformatics Programs (10 min.)
• Pjotr Prins - BioLib: Sharing high performance code between BioPerl, BioPython, BioRuby, R/Bioconductor and BioJAVA (15 min.)
• Peter Rice - EMBOSS: European Molecular Biology Open Software Suite (10 min.)
• Peter Cock - Biopython Project Update (10 min.)
• Andreas Prlic - BioJava 2009: an Open-Source Framework for Bioinformatics (10 min.)
• Jim Procter - Application of VAMSAS enabled tools for the investigation of protein evolution (10 min.)
• Steffen Möller - Debian adopts and disseminates Bioinformatics Open Source Software (5 min. Lightning Talk)

Regulatory Genomics

Click on the title to view the abstract.

• Finn Drablos - Computational discovery of composite motifs in DNA (15 min.)
• Sophie Schbath - R'MES (15 min.)
• Matias Piipari - Large-scale gene regulatory motif discovery and categorisation with NestedMICA (10 min.)
• Bartek Wilczynski - BNfinder: free software for effective Bayesian Network inference (15 min.)
• Lonnie Welch - Open Source Implementation of Batch-Extraction for Coding and Non-coding Sequences/An Open Source Framework for Bioinformatics Word Enumeration and Scoring (10 min.)
• François Fauteux - SEEDER: PERL MODULES FOR CIS-REGULATORY MOTIF DISCOVERY (10 min.)

Design Patterns Panel Discussion

On the Applicability of Design Patterns for the Bioinformatics Open Source Community

Click on the author's name to view the abstract submitted for the panel.

• Robert Hanmer - Moderator
• Lonnie Welch
• Aleksi Kallio

Schedule

Day 1

Time	Speaker	Title
9:00-9:15am	Kam Dahlquist	[Welcome]
9:15-10:15	Alan Ruttenberg	[Keynote] Semantic Web Technologies
10:15-10:45	Coffee Break
10:45-11:05	Jean-Stéphane Varré	[Multicore & GPGPU Computing] Biomanycores, a repository of interoperable open-source code for many-cores bioinformatics
11:25-11:40	Josh Buckner	[Multicore & GPGPU Computing] Enabling GPU Computing in the R Statistical Environment
11:25-11:40	Mikhail Fursov	[Multicore & GPGPU Computing] UGENE – A practical approach for complex computational analysis in molecular biology
11:40-11:48	Oswaldo Trelles	[Multicore & GPGPU Computing Lightning Talk] Qnorm: A library of parallel methods for gene-expression Q-normalization
11:48-12:08pm	Hajo N. Krabbenhöft	[Computational Grids] Taverna workflows across Grids, web services and the command line
12:08-12:23	Ann-Kristin Grimm	[Computational Grids] Grid-based expression QTL analysis
12:23-12:31	Joel Hedlund	[Computational Grids Lightning Talk] The Nordic BioGrid project -- Bioinformatics for the grid
12:31-2:00	Lunch
2:00-2:20	Allan Kuchinsky	[Visualization] Cytoscape Springs Forward: Re-architecture for Version 3.0
2:20-2:33	Frederik Decouttere	[Visualization] Bioinformatics simplified with seqpad
2:33-2:46	Bernat Gel	[Visualization] DASGenExp: an interactive web-based DAS client with client-side rendering
2:46-2:59	Kazuharu Arakawa	[OS Software] Web Service Interface for G-language Genome Analysis Environment
2:59-3:12	Sylvain Brohée	[OS Software] Best of both worlds : combining the user-friendliness of Wikis and the rigor of biological databases
3:12-3:30	Bartek Wilczynski	[Regulatory Genomics] BNfinder: free software for effective Bayesian Network inference
3:30-4:00	Coffee Break
4:00-4:20	Morris Swertz	[Data & Analysis Management] MOLGENIS by example: generating an extensible platform for genotype and phenotype experiments
4:20-4:40	Robert Murphy	[Data & Analysis Management] PSLID, the Protein Subcellular Location Image Database: Subcellular location assignments, annotated image collections, image analysis tools, and generative models of protein distributions
4:40-5:00	Mark Welsh	[Data & Analysis Management] BioHDF: Open binary file formats for large-scale data management – Project Update
5:00-5:15	Brad Chapman	[Data & Analysis Management] Lowering barriers to publishing biological data on the web
5:15-5:30	Kam Dahlquist	[Data & Analysis Management] XMLPipeDB: A Reusable, Open Source Tool Chain for Building Relational Databases from XML Sources
5:30-6:00	Lightning Talks and Birds of a Feather
7:00	B|F Board Meeting and No-host Dinner (location TBA)